If I use the shifter, I use the clutch. Always.
If I use sequential, I set it to Auto-clutch. The benefit is that you can still use the clutch manually with auto-clutch enabled.
The greatest benefit for me with using the clutch manually (whether I use shifter/sequential) is getting a fast, smooth, straight starting take-off with little to no wheelspin. This really helps prevent "false starts" and is a great advantage with patch-X.
The clutch also helps me keep the car stable during downshifts when using the shifter. Also, if I accidentally drop down a gear or two too low, I can just push in the clutch and correct my mistake before the car gets squirmy or completely wipes. Sometimes it's quicker to step on the clutch in that situation than to try to click back up on the sequential shifter...sometimes.
If the track has a lot of tight/slow corners (KY GP Long/Fern Bay Black), I use sequential so I can keep my hands on the wheel more. If I race a more "corner friendly" track (Westhill), I'm faster with the shifter/clutch. It all comes down to personal taste / personal skill in the end.